8ZKD | pdb_00008zkd

The Crystal Structure of the RON from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8ZKD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-05-16 Released: 2024-06-26 
• Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Pan, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.231 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of the RON from Biortus.

Wang, F., Cheng, W., Yuan, Z., Qi, J., Pan, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.9 kDa 
• Atom Count: 2,651 
• Modeled Residue Count: 298 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage-stimulating protein receptor beta chain	A	298	Homo sapiens	Mutation(s): 0  Gene Names: MST1R, PTK8, RON EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q04912 (Homo sapiens) Explore Q04912  Go to UniProtKB:  Q04912
PHAROS:  Q04912 GTEx:  ENSG00000164078

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.231 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.190 (DCC) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.193	α = 90
b = 98.193	β = 90
c = 46.873	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Pan, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release